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Pymc

K-DenseCommunityCreated by K-Dense Inc.

  • Skill
  • Tool integration
  • Science and research
  • MIT
  • Low risk
  • Has scripts

From the author

Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model comparison. Use for probabilistic modeling and uncertainty inference in PyMC.
— the description by K-Dense Inc.

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

This skill provides a structured environment for Bayesian modeling using PyMC 6.3.2. It covers the full lifecycle of probabilistic analysis, including model definition, prior predictive checks, MCMC sampling via NUTS, and posterior diagnostics. The skill includes helper scripts for evaluating model convergence, performing PSIS-LOO model comparison, and generating diagnostic reports, ensuring that users can rigorously assess uncertainty and predictive performance.

What it does

  • Defines generative Bayesian models with scientifically calibrated priors.
  • Executes NUTS MCMC sampling for posterior inference.
  • Performs prior and posterior predictive checks to validate model assumptions.
  • Provides diagnostic tools for assessing convergence, including R-hat and ESS.
  • Facilitates model comparison using PSIS-LOO and predictive model averaging.
  • Includes templates for linear, hierarchical, and count-based regression models.

When to use it

  • When performing probabilistic modeling and uncertainty quantification.
  • When comparing multiple candidate models for predictive performance.
  • When analyzing grouped or hierarchical data structures.
  • When you need to validate model convergence beyond simple visual inspection.
  • When building custom Bayesian models requiring specific likelihoods or priors.

Advantages

  • Integrates standard diagnostic workflows to identify sampling issues.
  • Supports complex hierarchical structures and non-centered parameterizations.
  • Provides robust model comparison metrics using ArviZ 1.3.
  • Encourages reproducible research by tracking seeds and data provenance.
  • Includes pre-built templates for common statistical modeling patterns.

Usage examples

“Run the hierarchical model template with 2 chains.”
Executes the hierarchical_model_template.py script using uv, generating posterior samples and diagnostic artifacts in the specified output directory.
“Check my model diagnostics for parameters alpha and beta.”
Runs the check_diagnostics helper on your inference data, reporting R-hat, ESS, and any sampler-specific warnings like divergences.
“Compare my linear and robust models using LOO.”
Uses the compare_models helper to rank models by ELPD and provides a reliability check for the PSIS-LOO estimates.

Install

  1. Download the skill as a ZIP:

    https://mp-staging.autogineer.com/agent-skills/k-dense-ai/pymc/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip pymc.zip -d .agents/skills

Documentation by K-Dense Inc.

PyMC Bayesian Modeling

Version and scope

Targets PyMC 6.3.2, PyTensor 3.3.2, and ArviZ 1.3.0. These are local Python APIs, with no service endpoint, credentials, or remote inference required. The native tests use the PyMC NUTS sampler on small synthetic models. Optional nutpie/JAX samplers, SMC, and production-scale convergence are not validated by those tests. Record the complete resolved environment, backend, seeds, preprocessing, and data provenance for a scientific run.

Local macOS validation used PYTENSOR_FLAGS="cxx=" after the C linker failed with library 'd64' not found; this disables PyTensor C compilation for that process. The Python library workflows passed under that setting; it does not establish that the C backend works on this host.

ArviZ 1 splits into base/stats/plots packages, re-exported by import arviz as az. PyMC returns an xarray DataTree despite the legacy return_inferencedata option name. az.summary(..., round_to="none") returns numerical columns; the default formats for display. Use az.plot_ppc_dist, az.plot_dist, and az.plot_trace_dist; save their returned PlotCollection, not a separate pyplot figure. az.hdi(..., prob=.95) uses prob, with bounds along ci_bound.

Workflow

  1. Define the estimand and predictive unit: another measurement, a new patient or group, or a future time block. Preserve units, missingness assumptions and grouping. Fit any scaling only on training data; reject constant columns.

  2. Build a generative model with scientifically calibrated priors and named dimensions. Check likelihood support, finite initial log probability, design rank, confounding and symmetries before sampling.

  3. Run a prior predictive check and inspect domain-relevant summaries before fitting. A broad prior is not automatically noninformative or plausible.

  4. Fit several independent chains with explicit seeds. For reproducible backend selection use nuts_sampler="pymc"; the automatic choice can prefer installed nutpie. nuts={...} replaces deprecated nuts_sampler_kwargs.

  5. Inspect rank R-hat, bulk/tail ESS, estimand-specific MCSE, divergences, energy BFMI and sampler-specific tree depth. Fix geometry and initialization before simply increasing draws. A clean screen does not prove convergence.

  6. Generate posterior predictive replicates and inspect residual structure, tails, zeros, group effects and time dependence relevant to the question. In-sample agreement is not external validation or parameter identifiability.

  7. Compare prior sensitivity and parameter recovery on synthetic data. Weakly informed scales, correlated parameters, separated logistic data, or mixture label switching can survive good MCMC diagnostics. A proper prior may make a posterior finite without the likelihood identifying its parameters.

  8. Predict using the correct training transform and uncertainty levels. Keep predictions separate from in-sample posterior_predictive. Restore model data before recomputing training likelihoods.

See standard_workflow.md for a complete bounded API smoke example, workflows.md for missing values, scaling, predictive scoring and serialization, and model_patterns.md for model structures.

Runnable templates

From the skill directory, run the synthetic linear or hierarchical template:

uv run --isolated --with "pymc==6.3.2" --with "arviz==1.3.0" --with "pytensor==3.3.2" --with matplotlib --with pandas --with h5netcdf --with h5py python assets/linear_regression_template.py --draws 80 --tune 80 --chains 2 --output-dir linear_smoke
uv run --isolated --with "pymc==6.3.2" --with "arviz==1.3.0" --with "pytensor==3.3.2" --with matplotlib --with pandas --with h5netcdf --with h5py python assets/hierarchical_model_template.py --draws 80 --tune 80 --chains 2 --output-dir hierarchical_smoke

These short commands intentionally test execution and artifacts; they are not adequate evidence of converged scientific estimates. For a real analysis, inspect priors before fitting and budget chains/draws around diagnostics and required MCSE. The templates default to four chains and longer runs, but those counts are not acceptance criteria by themselves.

The hierarchical template predicts an unseen group by drawing group effects from every hyperposterior draw, sharing each group effect across that group's new rows, then adding observation noise. Using only population means omits between-group uncertainty. Centered, non-centered, and partial parameterizations can each be appropriate; non-centering is not universally superior.

Diagnostic and comparison helpers

Import the modules from this skill's scripts/ directory (add that directory to sys.path when working elsewhere). Example fragments below assume fitted data:

from scripts.model_diagnostics import check_diagnostics, create_diagnostic_report
result = check_diagnostics(idata, var_names=["alpha", "beta", "sigma"])
create_diagnostic_report(idata, var_names=["alpha", "beta", "sigma"], output_dir="diagnostics")

check_diagnostics flags nonfinite statistics and insufficient chains. It reports missing HMC statistics as unavailable rather than claiming zero divergences. It uses recorded reached_max_treedepth, or an explicit max_treedepth matching the actual sampler; never infer the configured limit from the maximum observed value. The default ESS floor of 400 is pooled across chains, a screening floor, not a universal precision target. BFMI below 0.3 is a warning heuristic.

from scripts.model_comparison import compare_models, check_loo_reliability, model_averaging
models = {"linear": idata_linear, "robust": idata_robust}
check_loo_reliability(models, var_name="y_obs")
comparison = compare_models(models, var_name="y_obs")
mixture_draws, weights = model_averaging(models, var_name="y_obs", random_seed=42)

Compute pointwise log likelihood while the model contains the training data: pm.compute_log_likelihood(idata, model=model). Passing log_likelihood through idata_kwargs still works in 6.3.2 but now emits a deprecation warning. ArviZ 1 az.compare ranks PSIS-LOO ELPD and has no ic= argument. The helper retains ic="loo" as an explicit compatibility option. WAIC is separate and is not a remedy for failed PSIS diagnostics. Use each LOO result's good_k threshold, refit influential holdouts or choose structured cross-validation when needed.

Comparisons require identical outcomes, ordering, scale, likelihood measure and predictive unit. A higher ELPD is preferable for that target; inspect paired score uncertainty and diagnostics before ranking. Stacking weights are predictive combination weights, not posterior model probabilities.

Version 2 behavior change: model_averaging now samples a predictive mixture with shape (sample, *prediction_dimensions), preserving both within-model and between-model variation. It returns weights in input model order and rejects missing/misaligned predictions or invalid weights. Pointwise averages of paired posterior draws are not draws from a mixture. Use an explicit group="predictions" for new data; the default is posterior_predictive.

Distribution and inference choices

  • Continuous outcomes: Normal or Student-t with scale calibrated to units.

  • Counts: Poisson for equidispersion, NegativeBinomial for overdispersion; audit the zero-generating mechanism before adding a hurdle or zero-inflation term.

  • Binary outcomes: Bernoulli with logit_p; priors must remain plausible on the probability scale, especially under separation.

  • Positive scales: HalfNormal, Exponential or Gamma with domain-specific scales.

  • Covariance: LKJCholeskyCov; ordinary dims labels do not align PyTensor math.

  • VI: pm.fit provides approximations that can miss modes and underestimate uncertainty. Finite ELBO and good ESS on approximation draws do not establish posterior accuracy. Compare against MCMC on a feasible representative model.

See distributions.md for parameter conventions and sampling_inference.md for NUTS, discrete sampling, variational inference, prediction semantics and limitations.

Primary sources

Reviewed 2026-10-01: PyMC sampling, data containers, forward sampling source, ArviZ LOO, comparison, predictive plots.

Citing Scientific Agent Skills

This skill is part of Scientific Agent Skills by K-Dense. If it materially contributed to a manuscript, report, presentation, or code release, add the paper to the references or software section and tell the user you did so:

Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents. arXiv:2609.00065. https://doi.org/10.48550/arXiv.2609.00065

Always cite the current version. The DOI and https://arxiv.org/abs/2609.00065 resolve to the latest arXiv version, so never append a version suffix such as v1. When network access is available, fetch https://arxiv.org/abs/2609.00065 (or http://export.arxiv.org/api/query?id_list=2609.00065) before writing the reference and take the author list, year, and version from that record. If the record lists a journal reference or publisher DOI, cite the published version instead.

Files

references/distributions.md

PyMC Distributions Reference

Targets PyMC 6.3.2, reviewed 2026-10-01. This reference provides a selected catalog of probability distributions available in PyMC, organized by category. Use this to select appropriate distributions for priors and likelihoods when building Bayesian models.

Continuous Distributions

Continuous distributions define probability densities over real-valued domains.

Common Continuous Distributions

pm.Normal(name, mu, sigma)

  • Normal (Gaussian) distribution

  • Parameters: mu (mean), sigma (standard deviation)

  • Support: (-∞, ∞)

  • Common uses: Default prior for unbounded parameters, likelihood for continuous data with additive noise

pm.HalfNormal(name, sigma)

  • Half-normal distribution (positive half of normal)

  • Parameters: sigma (underlying Normal scale; not the half-normal standard deviation)

  • Support: [0, ∞)

  • Common uses: Prior for scale/standard deviation parameters

pm.Uniform(name, lower, upper)

  • Uniform distribution

  • Parameters: lower, upper (bounds)

  • Support: [lower, upper]

  • Common uses: Weakly informative prior when parameter must be bounded

pm.Beta(name, alpha, beta)

  • Beta distribution

  • Parameters: alpha, beta (shape parameters)

  • Support: [0, 1]

  • Common uses: Prior for probabilities and proportions

pm.Gamma(name, alpha, beta)

  • Gamma distribution

  • Parameters: alpha (shape), beta (rate)

  • Support: (0, ∞)

  • Common uses: Prior for positive parameters, rate parameters

pm.Exponential(name, lam)

  • Exponential distribution

  • Parameters: lam (rate parameter)

  • Support: [0, ∞)

  • Common uses: Prior for scale parameters, waiting times

pm.LogNormal(name, mu, sigma)

  • Log-normal distribution

  • Parameters: mu, sigma (parameters of underlying normal)

  • Support: (0, ∞)

  • Common uses: Prior for positive parameters with multiplicative effects

pm.StudentT(name, nu=nu, mu=mu, sigma=sigma)

  • Student's t-distribution

  • Parameters: nu (degrees of freedom), mu (location), sigma (scale)

  • Support: (-∞, ∞)

  • Common uses: Robust alternative to normal for outlier-resistant models

pm.Cauchy(name, alpha, beta)

  • Cauchy distribution

  • Parameters: alpha (location), beta (scale)

  • Support: (-∞, ∞)

  • Common uses: Heavy-tailed alternative to normal

pm.HalfStudentT(name, nu, sigma)

  • Positive half-Student-t distribution

  • Common uses: Heavy-tailed prior for scale parameters

Specialized Continuous Distributions

pm.Laplace(name, mu, b) - Laplace (double exponential) distribution

pm.AsymmetricLaplace(name, kappa, mu, b) - Asymmetric Laplace distribution

pm.InverseGamma(name, alpha, beta) - Inverse gamma distribution

pm.Weibull(name, alpha, beta) - Weibull distribution for reliability analysis

pm.Logistic(name, mu, s) - Logistic distribution

pm.LogitNormal(name, mu, sigma) - Logit-normal distribution for (0,1) support

pm.Pareto(name, alpha, m) - Pareto distribution for power-law phenomena

pm.ChiSquared(name, nu) - Chi-squared distribution

pm.ExGaussian(name, mu=mu, sigma=sigma, nu=nu) - Exponentially modified Gaussian

pm.VonMises(name, mu, kappa) - Von Mises (circular normal) distribution

pm.SkewNormal(name, mu=mu, sigma=sigma, alpha=alpha) - Skew-normal distribution

pm.Triangular(name, lower=lower, c=c, upper=upper) - Triangular distribution

pm.Gumbel(name, mu, beta) - Gumbel distribution for extreme values

pm.PolyaGamma(name, h, z) - Polya-gamma distribution for data augmentation patterns

pm.Rice(name, nu, sigma) - Rice (Rician) distribution

pm.Moyal(name, mu, sigma) - Moyal distribution

pm.Kumaraswamy(name, a, b) - Kumaraswamy distribution (Beta alternative)

pm.Wald(name, mu, lam) - Wald / inverse Gaussian distribution

pm.Interpolated(name, x_points, pdf_points) - Custom distribution from interpolation

Discrete Distributions

Discrete distributions define probabilities over integer-valued domains.

Common Discrete Distributions

pm.Bernoulli(name, p)

  • Bernoulli distribution (binary outcome)

  • Parameters: p (success probability)

  • Support: {0, 1}

  • Common uses: Binary classification, coin flips

pm.Binomial(name, n, p)

  • Binomial distribution

  • Parameters: n (number of trials), p (success probability)

  • Support: {0, 1, ..., n}

  • Common uses: Number of successes in fixed trials

pm.Poisson(name, mu)

  • Poisson distribution

  • Parameters: mu (rate parameter)

  • Support: {0, 1, 2, ...}

  • Common uses: Count data, rates, occurrences

pm.Categorical(name, p)

  • Categorical distribution

  • Parameters: p (probability vector)

  • Support: {0, 1, ..., K-1}

  • Common uses: Multi-class classification

pm.DiscreteUniform(name, lower, upper)

  • Discrete uniform distribution

  • Parameters: lower, upper (bounds)

  • Support: {lower, ..., upper}

  • Common uses: Uniform prior over finite integers

pm.NegativeBinomial(name, mu, alpha)

  • Negative binomial distribution

  • Parameters: mu (mean), alpha (dispersion)

  • Support: {0, 1, 2, ...}

  • Common uses: Overdispersed count data

pm.Geometric(name, p)

  • Geometric distribution

  • Parameters: p (success probability)

  • Support: {1, 2, 3, ...}

  • Common uses: Trial count through the first success (includes that success)

Specialized Discrete Distributions

pm.BetaBinomial(name, alpha, beta, n) - Beta-binomial (overdispersed binomial)

pm.HyperGeometric(name, N, k, n) - Hypergeometric distribution

pm.DiscreteWeibull(name, q, beta) - Discrete Weibull distribution

pm.OrderedLogistic(name, eta, cutpoints) - Ordered logistic for ordinal data

pm.OrderedProbit(name, eta, cutpoints) - Ordered probit for ordinal data

Multivariate Distributions

Multivariate distributions define joint probability distributions over vector-valued random variables.

Common Multivariate Distributions

pm.MvNormal(name, mu, cov)

  • Multivariate normal distribution

  • Parameters: mu (mean vector), cov (covariance matrix)

  • Common uses: Correlated continuous variables, Gaussian processes

pm.Dirichlet(name, a)

  • Dirichlet distribution

  • Parameters: a (concentration parameters)

  • Support: Simplex (sums to 1)

  • Common uses: Prior for probability vectors, topic modeling

pm.Multinomial(name, n, p)

  • Multinomial distribution

  • Parameters: n (number of trials), p (probability vector)

  • Common uses: Count data across multiple categories

pm.DirichletMultinomial(name, n, a)

  • Dirichlet-multinomial distribution

  • Common uses: Overdispersed categorical counts

pm.MvStudentT(name, nu=nu, mu=mu, scale=scale)

  • Multivariate Student's t-distribution

  • Parameters: nu (degrees of freedom), mu (location), scale (scale matrix; covariance is nu/(nu-2) times this matrix for nu > 2)

  • Common uses: Robust multivariate modeling

Specialized Multivariate Distributions

pm.LKJCorr(name, n, eta) - LKJ correlation matrix prior (for correlation matrices)

pm.LKJCholeskyCov(name, n=n, eta=eta, sd_dist=sd_dist) - LKJ prior with Cholesky decomposition

pm.OrderedMultinomial(name, eta, cutpoints, n) - Ordered multinomial outcomes

pm.StickBreakingWeights(name, alpha, K) - Stick-breaking weights for mixture models

pm.ZeroSumNormal(name, sigma) - Normal prior constrained to sum to zero

pm.Wishart(name, nu, V) - Wishart distribution (for covariance matrices; prefer LKJ-based priors for most covariance models)

There is no public pm.InverseWishart in PyMC 6.3.2. Prefer an explicit scientifically justified covariance model, usually LKJ with marginal scales.

pm.WishartBartlett(name, S, nu) - Wishart with Bartlett decomposition

pm.MatrixNormal(name, mu=mu, rowcov=rowcov, colcov=colcov) - Matrix normal distribution

pm.KroneckerNormal(name, mu=mu, covs=covs, sigma=sigma) - Kronecker-structured normal

pm.CAR(name, mu, W, alpha, tau) - Conditional autoregressive (spatial)

pm.ICAR(name, W, sigma) - Intrinsic conditional autoregressive (spatial)

Mixture Distributions

Mixture distributions combine multiple component distributions.

pm.Mixture(name, w, comp_dists)

  • General mixture distribution

  • Parameters: w (weights), comp_dists (component distributions)

  • Common uses: Clustering, multi-modal data

pm.NormalMixture(name, w, mu, sigma)

  • Mixture of normal distributions

  • Common uses: Mixture of Gaussians clustering

Zero-Inflated and Hurdle Models

pm.ZeroInflatedPoisson(name, psi, mu) - Excess zeros in count data

pm.ZeroInflatedBinomial(name, psi, n, p) - Zero-inflated binomial

pm.ZeroInflatedNegativeBinomial(name, psi, mu, alpha) - Zero-inflated negative binomial

pm.HurdlePoisson(name, psi, mu) - Hurdle Poisson (two-part model)

pm.HurdleNegativeBinomial(name, psi, mu, alpha) - Hurdle negative binomial for overdispersed counts with structural zeros

pm.HurdleGamma(name, psi, alpha, beta) - Hurdle gamma

pm.HurdleLogNormal(name, psi, mu, sigma) - Hurdle log-normal

Time Series Distributions

Distributions designed for temporal data and sequential modeling.

pm.AR(name, rho=rho, sigma=sigma, init_dist=init_dist)

  • Autoregressive process

  • Parameters: rho (AR coefficients), sigma (innovation std), init_dist (initial distribution)

  • Common uses: Time series modeling, sequential data

pm.GaussianRandomWalk(name, mu=mu, sigma=sigma, init_dist=init_dist)

  • Gaussian random walk

  • Parameters: mu (drift), sigma (step size), init_dist (initial value)

  • Common uses: Cumulative processes, random walk priors

pm.MvGaussianRandomWalk(name, mu=mu, cov=cov, init_dist=init_dist)

  • Multivariate Gaussian random walk

pm.MvStudentTRandomWalk(name, nu=nu, mu=mu, scale=scale, init_dist=init_dist)

  • Heavy-tailed multivariate random walk

pm.GARCH11(name, omega=omega, alpha_1=alpha_1, beta_1=beta_1, initial_vol=initial_vol)

  • GARCH(1,1) volatility model

  • Common uses: Financial time series, volatility modeling

pm.EulerMaruyama(name, dt, sde_fn, sde_pars, init_dist=init_dist)

  • Stochastic differential equation via Euler-Maruyama discretization

  • Common uses: Continuous-time processes

Special Distributions

pm.Deterministic(name, var)

  • Deterministic transformation (not a random variable)

  • Use for computed quantities derived from other variables

pm.Potential(name, logp)

  • Add arbitrary log-probability contribution; ignored by prior/posterior forward sampling, so a Potential alone does not define a generative likelihood

  • Use for custom likelihood components or constraints

pm.Flat(name)

  • Improper flat prior (constant density); cannot draw prior predictive samples

  • Use sparingly; can cause sampling issues

pm.HalfFlat(name)

  • Improper flat prior on positive reals; cannot draw prior predictive samples

  • Use sparingly; can cause sampling issues

Distribution Modifiers

pm.Truncated(name, dist, lower, upper)

  • Truncate a supported univariate .dist() distribution to specified bounds; support and inverse-CDF/rejection-sampling limitations depend on the base distribution

pm.Censored(name, dist, lower, upper)

  • Handle censored observations (observed bounds, not exact values)

pm.CustomDist(name, ..., logp, random)

  • Define custom distributions with user-specified log-probability and random sampling functions

pm.Simulator(name, fn, params, ...)

  • Custom distributions via simulation (for likelihood-free inference)

Usage Tips

Choosing Priors
  1. Scale parameters (σ, τ): Use HalfNormal, HalfCauchy, Exponential, or Gamma

  2. Probabilities: Use Beta or Uniform(0, 1)

  3. Unbounded parameters: Use Normal or StudentT (for robustness)

  4. Positive parameters: Use LogNormal, Gamma, or Exponential

  5. Correlation/covariance matrices: Prefer LKJCholeskyCov for covariance models; use LKJCorr when only correlations are needed

  6. Count data: Use Poisson or NegativeBinomial (for overdispersion)

Shape Broadcasting

PyMC distributions support NumPy-style broadcasting. Use the shape parameter to create vectors or arrays of random variables:

# Vector of 5 independent normals
beta = pm.Normal('beta', mu=0, sigma=1, shape=5)

# 3x4 matrix of independent gammas
tau = pm.Gamma('tau', alpha=2, beta=1, shape=(3, 4))
Using dims for Named Dimensions

Instead of shape, use dims for more readable models:

with pm.Model(coords={'predictors': ['age', 'income', 'education']}) as model:
    beta = pm.Normal('beta', mu=0, sigma=1, dims='predictors')

Parameterization and scientific caveats

  • Entries list important parameters, not exhaustive positional signatures. Prefer keywords: several distributions have keyword-only parameters. Catalog names and constructor signatures were checked against released source; specialized distributions were not all fit or sampled in this review.

  • NegativeBinomial has variance mu + mu**2 / alpha. InverseGamma beta is a scale, while Gamma beta is a rate. PolyaGamma needs the optional polyagamma package for relevant numerical operations.

  • In zero-inflated models psi is the weight on the ordinary count component, not the probability of a structural zero. In hurdle models it is the weight on the positive component. HurdleGamma/HurdleLogNormal are intended as observed likelihoods or forward-sampled RVs; ordinary MCMC does not correctly sample their mixed point-mass/continuous latent support.

  • LKJCholeskyCov(..., compute_corr=True) returns (chol, corr, stds) by default. LKJCorr ordinarily returns packed upper-triangle correlations, not a full correlation matrix. eta=1 is uniform over correlation matrices, not uniform independent marginal correlations for arbitrary dimension.

  • pm.Censored is not pm.Truncated: censoring puts probability mass at recorded limits; truncation conditions on being included inside limits. Selection and measurement processes decide the correct likelihood.

  • A density definition without a random/generative implementation can support fitting but not meaningful forward simulation. Check CustomDist event/batch shapes, log-density normalization and gradient behavior independently.

  • Ordinary dims names annotate arrays; they do not align symbolic arithmetic. Multivariate event dimensions and batch dimensions have different meanings.

Sources: distribution catalog, released distribution source, forward sampling source.

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Declares allowed tools, Needs network access, Needs Python

The author says: Requires Python 3.12+ with PyMC 6.3.2, PyTensor 3.3.2 and ArviZ 1.3-compatible dependencies; NumPy, pandas, Matplotlib, h5netcdf and h5py for bundled helpers/artifacts. Network access for installation only. Optional nutpie, NumPyro and BlackJAX samplers need separate dependencies.

Security

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Attribution and licence

Created by
K-Dense Inc.
Publisher
K-Dense (Community)
Source
K-Dense-AI/scientific-agent-skills · skills/pymc · commit a25cf9e
Licence
MIT License (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE.md)
  • ATTRIBUTION.md (written by AutoGineer)
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